Thank you Matt! Hui
________________________________ From: Matthew Knepley [[email protected]] Sent: Friday, April 17, 2015 3:10 PM To: Sun, Hui Cc: Barry Smith; [email protected] Subject: Re: [petsc-users] install petsc with valgrind On Fri, Apr 17, 2015 at 5:09 PM, Sun, Hui <[email protected]<mailto:[email protected]>> wrote: I'm not sure if I'm doing the right thing. But I have just export PATH=$PATH:dir_to_valgind_bin And I rerun the command: -@${PETSC_DIR}/bin/petscmpiexec -valgrind -n ${NP} ./test -mx ${ND} -my ${ND} -mz ${ND} -ksp_monitor_short -ksp_type fgmres -pc_type asm Then it seems to output something, for example: ==66450== Invalid write of size 8 ==66450== at 0x100055225: Schur_SetMatrix (in ./test) ==66450== by 0x10004F218: StokesSetup (in ./test) ==66450== by 0x1000DC582: main (in ./test) ==66450== Address 0x7fff5f93fb28 is on thread 1's stack ==66450== in frame #0, created by Schur_SetMatrix (???) ==66450== Yes, this worked, and it shows you have a memory overwrite in your code. You have no line numbers because you deleted the *.o files without running dsymutil. And before those output, it has the following lines: --66450-- run: /usr/bin/dsymutil "./test" warning: (x86_64) /Users/hus003/projects/LS_BDRY/test/test.o unable to open object file warning: no debug symbols in executable (-arch x86_64) --66450-- run: /usr/bin/dsymutil "/Users/hus003/Documents/software/petsc-valgrind/petsc-valgrind-debug/lib/libpetsc.3.05.3.dylib" --66450-- run: /usr/bin/dsymutil "/Users/hus003/Documents/software/petsc-valgrind-install/lib/libmpicxx.12.dylib" --66450-- run: /usr/bin/dsymutil "/Users/hus003/Documents/software/petsc-valgrind-install/lib/libmpifort.12.dylib" --66450-- run: /usr/bin/dsymutil "/Users/hus003/Documents/software/petsc-valgrind-install/lib/libmpi.12.dylib" --66450-- run: /usr/bin/dsymutil "/Users/hus003/Documents/software/petsc-valgrind-install/lib/libpmpi.12.dylib" Does it mean that it's working? But what does these two warnings mean? These warnings mean that symbols are missing from those libraries, which is no surprise. matt Best, Hui ________________________________________ From: Barry Smith [[email protected]<mailto:[email protected]>] Sent: Friday, April 17, 2015 2:57 PM To: Matthew Knepley Cc: Sun, Hui; [email protected]<mailto:[email protected]> Subject: Re: [petsc-users] install petsc with valgrind Or make sure valgrind is in your path > On Apr 17, 2015, at 4:56 PM, Matthew Knepley > <[email protected]<mailto:[email protected]>> wrote: > > As I said, it cannot find valgrind in your path. Remove it or install > valgrind. > > Matt > > On Fri, Apr 17, 2015 at 4:55 PM, Sun, Hui > <[email protected]<mailto:[email protected]>> wrote: > Thank you, Matt and Barry. I was trying to run the following: > -@${PETSC_DIR}/bin/petscmpiexec -valgrind -n ${NP} ./test -mx ${ND} -my ${ND} > -mz ${ND} -ksp_monitor_short -ksp_type fgmres -pc_type asm > > where NP=2, ND=32 > > And in the makefile I have specified the following: > include ${PETSC_DIR}/lib/petsc/conf/variables > include ${PETSC_DIR}/lib/petsc/conf/rules > include ${PETSC_DIR}/lib/petsc/conf/test > > Best, > Hui > > > ________________________________________ > From: Barry Smith [[email protected]<mailto:[email protected]>] > Sent: Friday, April 17, 2015 2:50 PM > To: Sun, Hui > Cc: [email protected]<mailto:[email protected]> > Subject: Re: [petsc-users] install petsc with valgrind > > Please please please always show WHAT YOU RAN with the error message. > Otherwise we just must guess > > > > On Apr 17, 2015, at 3:58 PM, Sun, Hui > > <[email protected]<mailto:[email protected]>> wrote: > > > > Thank you Barry. I just have it installed. And I was running a code, and > > got the following error message: > > > > HYDU_create_process (utils/launch/launch.c:75): execvp error on file > > valgrind: (No such file or directory) > > > > =================================================================================== > > = BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES > > = PID 66059 RUNNING AT math178.ucsd.edu<http://math178.ucsd.edu> > > = EXIT CODE: 255 > > = CLEANING UP REMAINING PROCESSES > > = YOU CAN IGNORE THE BELOW CLEANUP MESSAGES > > =================================================================================== > > > > What does this mean? > > > > Best, > > Hui > > > > ________________________________________ > > From: Barry Smith [[email protected]<mailto:[email protected]>] > > Sent: Friday, April 17, 2015 1:08 PM > > To: Sun, Hui > > Cc: [email protected]<mailto:[email protected]> > > Subject: Re: [petsc-users] install petsc with valgrind > > > > The development copy of PETSc allows using --prefix with MPICH > > http://www.mcs.anl.gov/petsc/developers/index.html > > > > > > > >> On Apr 17, 2015, at 2:38 PM, Sun, Hui > >> <[email protected]<mailto:[email protected]>> wrote: > >> > >> Hello, > >> > >> I want to install petsc with valgrind. And I read some documentations, > >> which suggests me to do > >> ./configure --download-mpich --with-valgind-dir=… > >> > >> However, I also want to specify --prefix, but petsc doesn't allow me, > >> because --download-mpich option does not work with --prefix install. > >> > >> Is there anyway that I can have petsc --prefix, together with valgrind? > >> > >> Best, > >> Hui > > > > > > -- > What most experimenters take for granted before they begin their experiments > is infinitely more interesting than any results to which their experiments > lead. > -- Norbert Wiener -- What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead. -- Norbert Wiener
